i noticed that some of my apps are in the background in unity-panel.
the apps are vmware-workstation,jupiter, empathy
this is what i mean

as you can see on the left some of my apps are running but in the background
if i didn't set my unity-panel to see-through i wouldn't have noticed it.
if i restart my laptop and start empathy it doesn't go in the background and also when
i run compiz --replace the apps are back in the foreground this happens a lot when i am working my apps are suddenly in the unity-panel background?

how to fix that (apps in the unity-panel background i find it really annoying, i have to taskkill some apps cause when i run it again i get "another instant is already running" err box
–
blade19899Feb 26 '12 at 14:07

Well, I copied it from a tutorial on getting VMWare workstation to show up in the panel, but Im guessing Unity has some sort of whitelist blacklist to determine what shows up in the panel, probably to keep a consistent look and feel. After running that command, Chrome and Google Talk showed up as well. I seriously just copied it from another post, and remembered this post and thought it would be helpful.

Welcome to AskUbuntu! Whilst this may theoretically answer the question, it would be preferable to include the essential parts of the answer here, and provide the link for reference.
–
OyiboNov 7 '12 at 7:43